param	value
verbose	FALSE
inputFile	../inst/testData/QI_2.0/peptide_measurements1.csv
resultsFileLabel	SQ_Results
outputDir	../inst/testData/QI_2.0/SQ_Results
proteinFastaFile	NA
scaffoldPTMSpectrumReportFile	NA
selectedProteinName	.
selectedModifName	
fdrCutoff	0.01
precursorMassFilter1	-1.52443738954182
precursorMassFilter2	0.943356907230989
cvCutOff	Inf
minNbPeptidesPerProt	1
maxNbPtmsPerPeptide	99999
minPeptideLength	1
normAC	.
eBayes	FALSE
SNonPairWiseStatTest	FALSE
expDesignTag	NA
proteinQuant	TRUE
ratioCutOff	1
deFdrCutoff	0.01
iBAQ	FALSE
top3	FALSE
isSaveRObject	FALSE
test	FALSE
pdfFilePath	../inst/testData/QI_2.0/SQ_Results/SQ_Results.pdf
peptideTsvFilePath	../inst/testData/QI_2.0/SQ_Results/SQ_Results_PEPTIDE.tsv
proteinTsvFilePath	../inst/testData/QI_2.0/SQ_Results/SQ_Results_PROTEIN.tsv
paramsFilePath	../inst/testData/QI_2.0/SQ_Results/SQ_Results_SQ_PARAMS.TXT
rDataFilePath	../inst/testData/QI_2.0/SQ_Results/SQ_Results_SQ.rData
